However, Eclipse RPM (Fedora 24+, RHEL 7.2+) users may encounter use constraint violations due to javax.servlet/javax.servlet-api conflicts between Orbit bundles and rpm-installed jars. In that case... I'm not sure what the solution is other than perhaps trying the Tasktop thing.

This connector is no longer supported. A new, supported JIRA connector is available in Tasktop Dev and includes a migrator to help you migrate your task list, contexts, and configuration from the Atlassian connector.

The Atlassian JIRA plugin works perfectly fine via the update site - update.atlassian.com/atlassian-eclipse-plugin/rest/e3.7 and is still suitable for anyone not wanting to pay for a commercial plugin.

We are running various versions of Eclipse (including MyEclipse 2016 CI) and the plugin via the update site works perfectly fine.

Suggestion: You should really mention in your comments that your plugin is a commercial plugin and perhaps also show license costs on your site.